Genetic susceptibility for more than forty diseases, most of them autoimmune in nature, is associated with genes encoded within the major histocompatibility complex (MHC), particularly the class I (HLA-A, B, C) and class II (Ia, HLA-D) MHC molecules. In many cases, the disease associations are strongest with HLA class II DR and DQ, suggesting that the DR/DQ subregion may be more important than other parts of the HLA region for autoimmunity dysfunction. Due to strong linkage disequilibrium in this genomic region for some populations, it is difficult to determine the specific genes involved in disease susceptibility.
In some cases, this difficulty can be circumvented by studying disease association in various ethnic groups. For example, in African populations, opportunities for ancestral intra-HLA recombinations (crossovers) have been numerous and haplotypic diversity is greater. In these populations, linkage disequilibria between specific HLA-DR and -DQ alleles is often weaker, which can help determine which region (DR or DQ) is more specifically involved in disease susceptibility. In addition, for some autoimmune diseases, complementation of HLA-DQA1 and -DQB1 alleles seems predisposed to disease as strongly as cis located alleles, thus suggesting the involvement of the DQ heterodimer itself rather than HLA-DR or another linked gene. The relatively limited number of haplotypic combinations found in all ethnic groups means that these strategies are not always applicable. Finer analyses of the association between HLA region genes and disease could therefore benefit from the definition of additional polymorphisms in the DR and DQ regions.
Due to their high degree of polymorphism in most mammalian species, microsatellite markers such as the (CA).sub.n, repeats, or GT on the complementary strand, are candidates for use in related gene mapping studies. The (CA).sub.n repeat sequences are estimated to occur every 30 kb in the haploid human genome. However, such repetitive elements are typically quite unstable, giving rise to very high mutation rates. Because of these high mutation rates, the utility of multialleleic markers for linkage disequilibrium studies has been uncertain. Thus, one would not expect that specific alleles of multiallelic markers would be significantly associated with particular genes.
Although HLA typing provides valuable information regarding disease susceptibility and suitability of tissue/organ transplantation donors, traditional methods of obtaining this information are laborious and expensive. One commonly used approach employs serological evaluation. To do so, HLA class I and II antigens are typed using a complement mediated lymphocytotoxicity test using purified T or B lymphocytes. HLA class I and II specific antisera are purified using naturally immunized individuals, in general multipare women.
Although HLA typing using serological methods to identify class I (A, B, and C) antigens are widely used, DNA-based methods have become more widespread to type HLA class II antigens (DR, DQ, and DP). The most common DNA-based method used is oligotyping. In this method, the polymerase chain reaction (PCR) is combined with dot-blot hybridization with sequence-specific oligonucleotide probes (SSOP) (e.g. forward or reverse dot blotting). PCR-SSP (sequence specific primer) and PCR-SSCP (single strand comformation polymorphism) methods represent other common DNA typing techniques used for HLA typing.
Our co-pending application Ser. No. 08/391,374, now abandoned discloses the unexpected finding that a polymorphic microsatellite marker in the HLA DQ region of the genome gives rise to distinct alleles which are strongly associated with specific HLA DQ alleles. This finding indicates that microsatellite markers in the HLA region can be useful in predicting HLA type. As HLA typing provides valuable information regarding disease susceptibility and suitability of donor tissue for transplantation, microsatellite markers which can predict HLA type are therefore useful in these capacities as well. Additional microsatellite markers from the HLA region are herein disclosed, providing further basis for a novel method of HLA typing which is simple, rapid, and inexpensive relative to traditional HLA typing methods.